def get_bioc_relations(self, docid, relations):
# <relation id="5618#7534">
# <infon key="Gene1">5618</infon>
# <infon key="Gene2">7534</infon>
# <infon key="relation">PPIm</infon>
# </relation>
biocDoc=BioCDocument()
biocDoc.id = docid
biocDoc.relations=[]
for rel in relations:
bioc_rel = BioCRelation()
rel_list = list(rel)
infon = {}
infon["relation"] = "PPIm"
infon["Gene1"] = rel_list[0]
infon["Gene2"] = rel_list[0]
if len(rel_list) == 2:
infon["Gene2"] = rel_list[1]
bioc_rel.id="{}#{}".format(infon["Gene1"], infon["Gene2"])
bioc_rel.infons=infon
biocDoc.relations.append(bioc_rel)
return biocDoc
def brat2bioc_doc(bratdoc: BratDocument) -> BioCDocument:
biocdoc = BioCDocument()
biocdoc.id = bratdoc.id
biocdoc.text = bratdoc.text
# entity
for bratentity in bratdoc.entities:
biocdoc.add_annotation(brat2bioc_entity(bratentity))
# relation
for bratrelation in bratdoc.relations:
biocdoc.add_relation(brat2bioc_relation(bratrelation))
# event
for bratevent in bratdoc.events:
biocdoc.add_relation(brat2bioc_event(bratevent))
# equiv
for i, brat_equiv in enumerate(bratdoc.equiv_relations):
brat_equiv.id = '%s%s' % (brat_equiv.id, i)
biocdoc.add_relation(brat2bioc_equiv(brat_equiv))
# attribute
for bratatt in bratdoc.attributes:
ann = biocdoc.get(bratatt.refid)
ann.infons['note_id'] = bratatt.id
ann.infons['attributes'] = ' '.join(sorted(bratatt.attributes))
# note
for bratnote in bratdoc.notes:
ann = biocdoc.get(bratnote.refid)
ann.infons['note_id'] = bratnote.id
ann.infons['type'] = bratnote.type
ann.infons['note'] = bratnote.text
return biocdoc
def __parse_document(self, tree):
document = BioCDocument()
document.id = tree.findtext('id')
document.infons = self.__parse_infons(tree)
for child in tree.findall('passage'):
document.add_passage(self.__parse_passage(child))
for child in tree.findall('annotation'):
document.add_annotation(self.__parse_annotation(child))
for child in tree.findall('relation'):
document.add_relation(self.__parse_relation(child))
return document
def convert_pubtator(input_path, output_path):
"""Convert pubtators annotation list to BioC XML
Keyword Arguments:
input_file -- the path of pubtators annotation file
output_file -- the path to output the BioC XML file
"""
# Set up BioCWriter to write specifically Pubtator
# Can change to incorporate other sources besides pubtator
writer = BioCWriter()
writer.collection = BioCCollection()
collection = writer.collection
collection.date = time.strftime("%Y/%m/%d")
collection.source = "Pubtator"
collection.key = "Pubtator.key"
opener = utilities.get_opener(output_path)
with opener(output_path, 'wb') as xml_file:
# Have to manually do this because hangs otherwise
# Write the head of the xml file
xml_shell = writer.tostring('UTF-8')
*xml_head, xml_tail = xml_shell.rstrip().split(b'\n')
for line in xml_head:
xml_file.write(line + b'\n')
article_generator = read_bioconcepts2pubtator_offsets(input_path)
# Write each article in BioC format
for article in tqdm.tqdm(article_generator):
document = BioCDocument()
document.id = article["pubmed_id"]
title_passage = BioCPassage()
title_passage.put_infon('type', 'title')
title_passage.offset = '0'
title_passage.text = article["title"]
abstract_passage = BioCPassage()
abstract_passage.put_infon('type', 'abstract')
abstract_passage.offset = article["abstract"]
abstract_passage.text = article["abstract"]
id_index = 0
for tag in article["title_annot"]:
title_passage.annotations.append(bioconcepts2pubtator_annotations(tag, id_index))
id_index += 1
for tag in article["abstract_annot"]:
abstract_passage.annotations.append(bioconcepts2pubtator_annotations(tag, id_index))
id_index += 1
document.add_passage(title_passage)
document.add_passage(abstract_passage)
step_parent = E('collection')
writer._build_documents([document], step_parent)
xml_file.write(tostring(step_parent[0], pretty_print=True))
step_parent.clear()
# Write the closing tag of the xml document
xml_file.write(xml_tail + b'\n')
def convert_pubtator(input_file, output_file=None):
"""Convert pubtators annotation list to BioC XML
Keyword Arguments:
input_file -- the path of pubtators annotation file
output_file -- the path to output the converted text
"""
if output_file is None:
output_file = "bioc-converted-docs.xml"
# Set up BioCWriter to write specifically Pubtator
# Can change to incorporate other sources besides pubtator
writer = BioCWriter()
writer.collection = BioCCollection()
collection = writer.collection
collection.date = time.strftime("%Y/%m/%d")
collection.source = "Pubtator"
collection.key = "Pubtator.key"
with open(output_file, 'wb') as g:
# Have to manually do this because hangs otherwise
# Write the head of the xml file
xml_header = writer.tostring('UTF-8')
xml_tail = '</collection>\n'
xml_head = xml_header[:-len(xml_tail)]
g.write(xml_head)
article_generator = bioconcepts2pubtator_offsets(input_file)
# Write each article in BioC format
for article in tqdm.tqdm(article_generator):
document = BioCDocument()
document.id = article["Document ID"]
title_passage = BioCPassage()
title_passage.put_infon('type', 'title')
title_passage.offset = '0'
title_passage.text = article["Title"]
abstract_passage = BioCPassage()
abstract_passage.put_infon('type', 'abstract')
abstract_passage.offset = str(article["Abstract"])
abstract_passage.text = article["Abstract"]
id_index = 0
for tag in article["Title_Annot"]:
title_passage.annotations.append(bioconcepts2pubtator_annotations(tag, id_index))
id_index += 1
for tag in article["Abstract_Annot"]:
abstract_passage.annotations.append(bioconcepts2pubtator_annotations(tag, id_index))
id_index += 1
document.add_passage(title_passage)
document.add_passage(abstract_passage)
step_parent = E('collection')
writer._build_documents([document], step_parent)
g.write(tostring(step_parent[0], pretty_print=True))
step_parent.clear()
# Write the closing tag of the xml document
g.write(xml_tail)
